Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

Lasse Maretty, Jacob Malte Jensen, Bent Petersen, Jonas Andreas Sibbesen, Siyang Liu, Palle Villesen, Laurits Skov, Kirstine González-Izarzugaza Belling, Christian Theil Have, Jose Maria Gonzalez-Izarzugaza, Marie Grosjean, Jette Bork-Jensen, Jakob Grove, Thomas D. Als, Shujia Huang, Yuqi Chang, Ruiqi Xu, Weijian Ye, Junhua Rao, Xiaosen GuoJihua Sun, Hongzhi Cao, Chen Ye, Johan van Beusekom, Thomas Espeseth, Esben N. Flindt, Rune M. Friborg, Anders E. Halager, Stephanie Le Hellard, Christina M. Hultman, Francesco Lescai, Shengting Li, Ole Lund, Peter Løngreen, Thomas Mailund, María Luisa Matey-Hernandez, Ole Mors, Christian N. S. Pedersen, Thomas Sicheritz-Pontén, Patrick F. Sullivan, Ali Syed, David Westergaard, Rachita Yadav, Ning Li, Xun Xu, Torben Hansen, Anders Krogh, Lars Bolund, Thorkild I. A. Sørensen, Oluf Pedersen, Ramneek Gupta, Simon Rasmussen, Søren Besenbacher, Anders D. Börglum, Jun Wang, Hans Eiberg, Karsten Kristiansen, Søren Brunak, Mikkel Heide Schierup

    Research output: Contribution to journalJournal articleResearchpeer-review

    636 Downloads (Pure)

    Abstract

    Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.
    Original languageEnglish
    JournalNature
    Volume548
    Pages (from-to)87-91
    ISSN0028-0836
    DOIs
    Publication statusPublished - 2017

    Bibliographical note

    Creative Commons
    The article for which you have requested permission has been distributed under a Creative Commons CC-BY license (please see the article itself for the license version number). You may reuse this material without obtaining permission from Nature Publishing Group, providing that the author and the original source of publication are fully acknowledged, as per the terms of the license.
    For license terms, please see http://creativecommons.org/

    Fingerprint Dive into the research topics of 'Sequencing and de novo assembly of 150 genomes from Denmark as a population reference'. Together they form a unique fingerprint.

    Cite this